Tony Abbott has played down the ongoing diplomatic turbulence between Indonesia and Australia over asylum seeker policy, describing the issue as a "passing irritant" in an otherwise "strong relationship".

Speaking before his visit to Indonesia next week, his first foreign mission as prime minister, Abbott said he hoped relations between the two states would not be "defined by this boats issue".

"That's one of the many reasons it is so important to stop the boats, because I don't want what is in so many respects our most important relationship to be needlessly complicated by this," Abbott told Fairfax radio on Monday.

The comments follow a week of diplomatic wrangling, which saw the Indonesian foreign minister, Marty Natalegawa, apparently take the forthright move of releasing details of a meeting between himself and his Australian counterpart, Julie Bishop, held at the UN headquarters in New York.

Natalegawa described elements of the Coalition's hardline Operation Sovereign Borders as "unilateral" and "worrying".

The plans, which include turning boats back and offering cash to Indonesians who offer information on people smugglers, "risk the close co-operation and trust that has been gained under the framework of the Bali process, and with that should be avoided", Natalegawa appeared to say in a statement.

But when Guardian Australia contacted the Indonesian ministry for foreign affairs it said the statement was not "an official press statement" and that it was unaware of how it had found its way into the public domain.

On Friday, Dewi Fortuna Anwar, a senior adviser to Indonesian vice-president Boediono, said if the boat turnaround policy was enacted it risked provoking a naval confrontation between the two countries.

Anwar told ABC radio: "I think it [boat turnaround] would create unnecessary conflict because I can just imagine that the Indonesian navy would not take kindly to that.

"So let's not be hypothetical about it. Any act by a foreign navy that infringes on a neighbouring country's territorial waters could cause incidents at sea and clearly that is not in the spirit of the framework of the treaty of co-operation that Indonesia and Australia have already signed."

Anwar added that she believed the issue of asylum was a "regional problem", echoing comments made earlier in the month by an Indonesian MP and member of the foreign affairs commission, Tantowi Yahya.

Abbott said on Friday that the Coalition would "do strong and sensible things that build on the strong relationship we already have with Indonesia".

He continued: "The key change since the swearing in is now anyone who gets here illegally by boat is out of the country to Nauru or Manus within 48 hours, and they're never coming back."

The 48-hour turnaround target has drawn criticism from medical groups, which say vital medical assessments of asylum seekers are unlikely to be adequately completed in that timeframe.

"We are especially concerned for unaccompanied minors but also children more broadly, as they are particularly vulnerable to the effects of detention and a lack of transparency is not conducive to protecting their health," Talley said.